Mercurial > repos > iuc > peakzilla
changeset 1:8badcbe5792c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla commit ce081671d5ad816158825b089a0e62682f5f7963
| author | iuc |
|---|---|
| date | Tue, 27 Feb 2024 10:34:27 +0000 |
| parents | ca3ec50bfd94 |
| children | |
| files | peakzilla.xml test-data/log.txt test-data/results.tsv test-data/results_1.tsv test-data/results_2.tsv |
| diffstat | 5 files changed, 33 insertions(+), 21 deletions(-) [+] |
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--- a/peakzilla.xml Mon Feb 26 10:55:19 2024 +0000 +++ b/peakzilla.xml Tue Feb 27 10:34:27 2024 +0000 @@ -2,7 +2,7 @@ <description>Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments</description> <macros> <token name="@TOOL_VERSION@">1.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="2.7">python</requirement> @@ -63,13 +63,22 @@ <outputs> <data name="results" format="tabular" label="${tool.name} on ${on_string}"/> <data name="log" format="txt" from_work_dir="log.txt" label="Log file for ${tool.name} on ${on_string}"> - <filter>log</filter> + <filter>outputs["log"]</filter> </data> <data name="negative_peaks" format="tabular" from_work_dir="negative_peaks.tsv" label="Negative peaks for ${tool.name} on ${on_string}"> - <filter>negative</filter> + <filter>outputs["negative"]</filter> </data> </outputs> <tests> + <test expect_num_outputs="1"> + <param name="chip_bed" value="chip.bed" /> + <param name="input_bed" value="input.bed" /> + <output name="results" file="results_1.tsv"> + <assert_contents> + <has_text text="Peak_1" /> + </assert_contents> + </output> + </test> <test expect_num_outputs="3"> <param name="chip_bed" value="chip.bed" /> <param name="input_bed" value="input.bed" /> @@ -79,7 +88,7 @@ <param name="score_cutoff" value="1" /> <param name="log" value="true" /> <param name="negative" value="true" /> - <output name="results" file="results.tsv"> + <output name="results" file="results_2.tsv"> <assert_contents> <has_text text="Peak_1" /> </assert_contents>
--- a/test-data/log.txt Mon Feb 26 10:55:19 2024 +0000 +++ b/test-data/log.txt Tue Feb 27 10:34:27 2024 +0000 @@ -1,15 +1,15 @@ -10:13:55 Loading tags ... -10:13:55 Tags in IP: 9953 -10:13:55 Tags in control: 9569 -10:13:55 Fragment size was set manually to 50 bp -10:13:55 Peak size is 101 bp -10:13:55 Estimating tag distribution using gaussian ... -10:13:55 Finding peaks in ChIP sample ... -10:13:55 Finding peaks in control sample ... -10:13:55 Calculating peak scores ... -10:13:55 Calculating FDR ... -10:13:55 1 peaks detected -10:13:55 Enrichment cutoff: 2.0 -10:13:55 Score cutoff: 1.0 -10:13:55 Writing input peaks to negative_peaks.tsv -10:13:55 Done! +11:01:24 Loading tags ... +11:01:24 Tags in IP: 9953 +11:01:24 Tags in control: 9569 +11:01:24 Fragment size was set manually to 50 bp +11:01:24 Peak size is 101 bp +11:01:24 Estimating tag distribution using gaussian ... +11:01:24 Finding peaks in ChIP sample ... +11:01:24 Finding peaks in control sample ... +11:01:24 Calculating peak scores ... +11:01:24 Calculating FDR ... +11:01:24 1 peaks detected +11:01:24 Enrichment cutoff: 2.0 +11:01:24 Score cutoff: 1.0 +11:01:24 Writing input peaks to negative_peaks.tsv +11:01:24 Done!
--- a/test-data/results.tsv Mon Feb 26 10:55:19 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -#Chromosome Start End Name Summit Score ChIP Control FoldEnrichment DistributionScore FDR -2R 18296030 18296130 Peak_1 18296080 924.99 1031.34 106.26 9.71 1.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_1.tsv Tue Feb 27 10:34:27 2024 +0000 @@ -0,0 +1,3 @@ +#Chromosome Start End Name Summit Score ChIP Control FoldEnrichment DistributionScore FDR +2R 18296016 18296218 Peak_1 18296117 677.90 1729.79 163.82 10.56 0.43 0.00 +2R 19461248 19461450 Peak_2 19461349 2.54 1063.25 104.50 10.17 0.00 0.00